rs587778762
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004628.5(XPC):āc.1229A>Gā(p.Glu410Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000164 in 1,461,698 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_004628.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XPC | NM_004628.5 | c.1229A>G | p.Glu410Gly | missense_variant | 9/16 | ENST00000285021.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XPC | ENST00000285021.12 | c.1229A>G | p.Glu410Gly | missense_variant | 9/16 | 1 | NM_004628.5 | P1 | |
XPC-AS1 | ENST00000627116.2 | n.457-7222T>C | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249282Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135236
GnomAD4 exome AF: 0.0000164 AC: 24AN: 1461698Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 727136
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Xeroderma pigmentosum, group C Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Mar 21, 2017 | - - |
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at